In 2002 the federal, state and provincial agencies that manage binational environmental activities under the 1987 Great Lakes Water Quality Agreement formally endorsed the formation of a Lake Huron Binational Partnership. The Partnership facilitates information sharing and priority setting for binational environmental protection and restoration activities of importance to the Lake Huron basin, as well as the development of partnerships to undertake efforts that cannot be accomplished by individual agencies alone.

The main binational priorities the Partnership is addressing are contaminants in fish and wildlife, ecosystem change (biodiversity, ecosystem function, and exotic species), and loss of fish and wildlife habitat.

The Lake Huron Binational Partnership also facilitates the sharing of information between countries on issues which are more local in nature. However, actions to address these local domestic issues are undertaken outside of the Partnership. On the Canadian side of the basin, domestic issues are dealt with through the Lake Huron Federal/Provincial Working Group. Water quality in Southeastern Lake Huron is one such domestic issue.